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VitisNet: Molecular Networks for Grapevine

Users can access the VitisNet (12X) files from this page in different formats. The picture files are pdf images of the Celldesigner files. Celldesigner and Cytoscape files can be loaded in the respective programs (for help, see the tutorial). Files need to be unzipped. Cytoscape sessions contain groups of processed networks that can be directly loaded and used in Cytoscape.

Click here for the tutorial

1 Metabolism

1.1 Carbohydrate metabolismDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
10010Glycolysis2232928
10020Citrate cycle791821
10030Pentose phosphate891721
10040Pentose/glucuronate interconversion621114
10051Fructose and mannose metabolism1172020
10052Galactose metabolism1761627
10053Ascorbate and aldarate metabolism5399
10500Starch and sucrose metabolism3734734
10530Aminosugars metabolism108810
10520Nucleotide sugars metabolism721618
10620Pyruvate metabolism2302819
10630Glyoxylate and dicarboxylate metabolism881819
10640Propanoate metabolism711112
10650Butanoate metabolism881819
10562Inositol phosphate metabolism701820

 

1.2 Energy metabolismDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
10190Oxidative phosphorylation3831057
10195Photosynthesis22352 
10196Photosynthesis antenna proteins3811 
10710Carbon fixation1822120
10720Reductive carboxylate cycle441014
10680Methane metabolism1331011
10910Nitrogen metabolism1172319
10920Sulfur metabolism481312
1.3 Lipid MetabolismDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
10061Fatty acid biosynthesis861336
10062Fatty acid elongation in mitochondria29729
10071Fatty acid metabolism1113040
10072Synthesis/degradation of ketone bodies2034
10100Biosynthesis of steroids1504976
10140C21-Steroid hormone metabolism18614
10561Glycerolipid metabolism1591918
10564Glycerophospholipid metabolism1503432
10565Ether lipid metabolism53139
10600Sphingolipid metabolism771315
10592Alpha-linolenic acid metabolism1062129
11040Biosynthesis of unsaturated fatty acids542027

 

1.4 Nucleotide metabolismDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
10230Purine metabolism1544962
10240Pyrimidine metabolism1133946

 

1.5 Amino Acid metabolismDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
10251Glutamate metabolism972825
10252Alanine and aspartate metabolism1172424
10260Glycine serine and threonine metabolism1163138
10271Methionine metabolism1353247
10272Cysteine metabolism841725
10280Val. leu. and ile degradation922034
10290Val. leu. and ile biosynthesis731426
10300Lysine biosynthesis855222
10330Arginine and proline metabolism651723
10340Histidine metabolism651819
10350Tyrosine metabolism1652739
10360Phenylalanine metabolism2241714
10380Tryptophan metabolism1967
10400Phenylalanine tyrosine and tryptophan biosynthesis1593035
10220Urea cycle and metabolism of amino groups1343341
1.6 Other amino acids metabolismDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
10410Beta-alanine metabolism591313
10450Selenoamino acid metabolism821517
10460Cyanoamino acid metabolism39816
10480Glutathione metabolism1593716
1.7 Glycan biosynthesis and metabolismDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
10510N-Glycan biosynthesis562322
10511N-Glycan degradation7808 
10540Lipopolysaccharides biosynthesis111013
10550Peptidoglycan biosynthesis20310
10563GPI-anchor biosynthesis221214
10602Glycosphingolipid biosynthesis17716
11030Glycan structures-biosynthesis11012648
1.8 Cofactors and vitamin metabolismDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
10730Thiamine metabolism221220
10740Riboflavin metabolism701315
10750Vitamin B6 metabolism19713
10760Nicotinate/nicotinamide metabolism281213
10770Pantothenate/CoA biosynthesis561519
10780Biotin metabolism868
10790Folate biosynthesis401724
10670One carbon pool by folate49159
10860Porphyrin and chlorophyll metabolism753239
10130Ubiquinone biosynthesis361725
1.9 Biosynthesis of secondary metabolitesDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
10900Terpenoid biosynthesis1921824
10902Monoterpenoid biosynthesis2172942
10904Diterpenoid biosynthesis781937
10908Zeatin biosynthesis611120
10906Carotenoid biosynthesis492233
10905Brassinosteroid biosynthesis21724
10940Phenylpropanoid biosynth.2432546
10941Flavonoid biosynthesis1902552
10942Anthocyanin biosynthesis72818
10943Isoflavonoid biosynthesis68717
10950Alkaloid biosynthesis I651723
10311Penicillin/cephalosp. Biosynthesis1355
11002Auxin biosynthesis992412
11012Iba metabolism21115
11013ABA biosynthesis18811
10966Glucosinolate biosynthesis401027
1.10 OtherDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
11000Single reactions1901538

2 Genetic information processing networks

2.1 TranscriptionDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
23020RNA polymerase9634 
23022Basal transcription factors6723 
23040Spliceosome280139 
2.2 TranslationDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
23010Ribosome612131 
20970Aminoacyl-tRNA biosynth.1222264
23013RNA transport26092 
23015mRNA surveillance pathway13542 
23008Ribosome biogenesis in Eukaryotes14159 
2.3 Folding, sorting degradationDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
23060Protein export6430 
24141Protein processing in endoplasmic reticulum27968 
24130SNARE interaction in vesicular transport6922 
23050Proteasome7547 
24120Ubiquitin mediated proteolysis204683
2.4 Replication and repairDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
23030DNA replication8238 
23410Base excision repair3221 
23420Nucleotide excision repair7236 
23430Mismatch repair4919 
23440Homologous recombination5119 
23450Non homologous end joining198 
24122Sulfur relay system1572
23018RNA degradation11548 

3 Environmental information processing

3.1 Signal transductionDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
34020Calcium signaling pathway1523222
34070Phosphatidylinositol signaling system831417
34150mTOR signaling pathway3217 
3.2 Hormone signalingDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
30001ABA signaling16810111
30003Auxin signaling3111491
30005Brassinosteroids signaling63242
30007Cytokinin signaling80741
30008Ethylene signaling2752473
30010Gibberellin signaling43281
30011Jasmonate signaling98714
3.3 Plant-specific signalingDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
34710Circadian rhythm7963 
34626Plant-pathogen interaction3601227
34627R proteins from Plant-pathogen interaction47211 
30009Flower development2041881

4 Cellular processes

4.1 Transport and catabolismDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
44140Regulation of autophagy30164
44145Phagosome14229 
44146Peroxisome95471
4.2 Cell motilityDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
44810Regulation of actin cytoskeleton3961171
4.3 Cell growth and deathDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
44110Cell cycle358238 
40006Cell wall5186211

5 Transport

5.1 Membrane transportDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
52010ABC transporters28493 
5.2 Hormone transportDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
50004Auxin transport58271
5.3 Transport systemDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
50110Protein coat229105 
50111Tethering factors11770 
50112Nuclear pore complex9028 
50113Thylakoid targeting pathway7115 
5.4 Transporter catalogDownload pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
50101Channels and pores451146 
50104Group translocators4210 
50105Transport electron carriers10938 
50108Accessory factors involved in transport17216 
50109Incompletely characterized transport systems38398 
50121Porters cat 1 to 619786 
50122Porters cat 7 to 1725950 
50123Porters cat 18 to 2922546 
50124Porters cat 30 to 6417070 
50125Porters cat 66 to 9423055 
50131Prim. active transp. A2-A422353 
50132Prim. active transp. A5-A820584 
50133Prim. active transp. A9-A1826299 
50134Prim. active transp. cat D117546 
50135Prim. active transp. D3-E215644 

6 Transcription factors

 Download pictures zip fileDownload Celldesigner zip fileDownload Cytoscape zip file
VVIDNetwork name#genes#proteins#mets
60001ABI3VP12525 
60002Alfin-like88 
60003AP2 EREBP158158 
60004ARF2929 
60005ARID1212 
60006ARR-B1515 
60007AS25251 
60008AUXIAA3131 
60009BBR66 
60010BES11111 
60011BHLH163163 
60012BZIP7373 
60013BHSH11 
60014C2C2-CO1414 
60015C2C2-DOF2525 
60016C2C2-GATA2525 
60017C2H2138138 
60018C3H9393 
60019C2C2-YABBY77 
60020CAMTA88 
60021CCAAT3535 
60022CPP77 
60023CSD44 
60024DBP77 
60025DDT1010 
60026E2F-DP88 
60027EIL55 
60028FHA2323 
60029G2-like4343 
60030GeBP88 
60031GIF44 
60032GRAS5353 
60033GRF1414 
60034HB102102 
60035HMG1818 
60036HRT11 
60037HSF2222 
60038Jumonji2929 
60039LFY11 
60040LIM1212 
60041LUG99 
60042MADS8181 
60043MBF166 
60044MYB179179 
60045MYBrelated7171 
60046NAC8686 
60047PBF-2-like22 
60048PHD8181 
60049PLATZ1212 
60050PseudoARR-B99 
60051RB22 
60052RWP-RK1212 
60053S1Fa-like33 
60054SAP11 
60055SBP2323 
60056SET PCG6464 
60057Sigma70-like66 
60058SNF24747 
60059SRS55 
60060TAZ87 
60061TCP2121 
60062Trihelix3737 
60063TUB1717 
60064ULT11 
60065VOZ22 
60066WRKY6969 
60067zf-MYND44 
60068zf-HD1818 
60069ZIM1414 
60070Orphans CCT88 
60071Orphans FAR-RED7171 
60072Orphans Response reg1616 
60073Orphans zf-b box1515 
60074Orphans zf-SWIM88 
60075Other BSD1212 
60076Other GTF77 
60077Other zf-AN11515 
60078Other zf-C3HC4279279 
60079Other zf-DHHC2525 
60080Other zf3939 
60081COAP1522 
60082GNAT3636 
60083IWS111 
60084MED22 
60085MTERF3939 
60086OFP1717 
60087Orphans KIP1 SANTA66 
60088Orphans WRC11 
60089Other Nozzle11 
60090RCD122 
60091SOH111 
60092SWIB1616 
60093TRAF3434 
60094SWI SNF SWI322 
60095Orphans PAH44 

Users of VitisNet should cite: VitisNet: “Omics” Integration through Grapevine Molecular Networks. Jérôme Grimplet, Grant R. Cramer, Julie A. Dickerson, Kathy Mathiason, John Van Hemert and Anne Y. Fennell, 2009, PLoS ONE: http://dx.plos.org/10.1371/journal.pone.0008365.

VitisNet Gene Annotation Reference file -The complete Vitis vinifera gene functional annotation and 8x to 12X sequence correspondence: Genes_annotation

Please reference: Grimplet J, J Van Hemert, P Carbonell-Bejerano, J Diaz-Riquelme, J Dickerson, A Fennell, M Pezzotti, JM Martinez-Zapater. 2012. Comparative analysis of grapevine whole-genome predictions, functional annotation, categorization and integration of the predicted gene sequences. BMC Research Notes 5:213 doi:10.1186/1756-0500-5-213

The 8X version of VitisNet can be accessed here

Cytoscape sessions

Files need to be unzip before use with Cytoscape

Raw Networks:
1. Metabolism Part 1Part 2
2. Genetic Information Processing
3. Environmental Information Processing
4. Cellular Processes
5. Transport
6. Transcription Factors Part 1Part 2

Tutorial files

-Mapping file for Affymetrix microarray:
GS_to_probeset.txt

-Model for input of abundance data:
expression_berry.txt

-Cytoscape style for visualization of berry tissues data:
berrystyle.props

-Citrate Cycle (TCA cycle)
vv10020CitrateCycle.xml

Cytoscape networks with molecular abundance in berry tissues:
from Grimplet et al., 2007 and Grimplet et al., 2009
1. Metabolism Part 1Part 2
2. Genetic Information Processing
3. Environmental Information Processing
4. Cellular Processes
5. Transport
6. Transcription Factors Part 1Part 2

Contacts:

Jerome Grimplet

Anne Fennell